wip

cases_files/tests/test_models.py

@@ -18,6 +18,7 @@
 @freeze_time("2012-01-14 12:00:01")
 class IndividualExternalFileTest(TestCase):
     def setUp(self):
+        super().setUp()
         self.maxDiff = None  # show full diff
 
     def test_create(self):
@@ -37,6 +38,7 @@ def test_update(self):
 @freeze_time("2012-01-14 12:00:01")
 class PedigreeExternalFileTest(TestCase):
     def setUp(self):
+        super().setUp()
         self.maxDiff = None  # show full diff
 
     def test_create(self):
@@ -56,6 +58,7 @@ def test_update(self):
 @freeze_time("2012-01-14 12:00:01")
 class IndividualInternalFileTest(TestCase):
     def setUp(self):
+        super().setUp()
         self.maxDiff = None  # show full diff
 
     def test_create(self):
@@ -79,6 +82,7 @@ def test_update(self):
 @freeze_time("2012-01-14 12:00:01")
 class PedigreeInternalFileTest(TestCase):
     def setUp(self):
+        super().setUp()
         self.maxDiff = None  # show full diff
 
     def test_create(self):

cases_import/tests/test_models.py

@@ -18,6 +18,7 @@
 @freeze_time("2012-01-14 12:00:01")
 class CaseImportActionTest(TestCase):
     def setUp(self):
+        super().setUp()
         self.maxDiff = None  # show full diff
 
     def test_create(self):
@@ -36,6 +37,7 @@ def test_update(self):
 
 class CaseImportBackgroundJobTest(TestCase):
     def setUp(self):
+        super().setUp()
         self.maxDiff = None  # show full diff
         self.user = self.make_user("test_user")
 

cases_import/tests/test_models_executor.py

@@ -21,7 +21,6 @@
 
 class ExecutorTestMixin:
     def _setUpExecutor(self, action, fac_kwargs=None):
-        super().setUp()
         self.user = self.make_user()
         self.caseimportaction = CaseImportActionFactory(
             action=action,
@@ -56,6 +55,7 @@ class ImportCreateTest(ExecutorTestMixin, TestCaseSnapshot, TestCase):
     """
 
     def setUp(self):
+        super().setUp()
         self._setUpExecutor(CaseImportAction.ACTION_CREATE)
 
     def test_run(self):
@@ -71,6 +71,7 @@ class ImportCreateWithDragenQcTest(ExecutorTestMixin, TestCaseSnapshot, TestCase
     """
 
     def setUp(self):
+        super().setUp()
         self.maxDiff = None
         self._setUpExecutor(
             CaseImportAction.ACTION_CREATE,
@@ -354,6 +355,7 @@ class ImportCreateWithSamtoolsQcTest(ExecutorTestMixin, TestCaseSnapshot, TestCa
     """
 
     def setUp(self):
+        super().setUp()
         self.maxDiff = None
         self._setUpExecutor(
             CaseImportAction.ACTION_CREATE,
@@ -421,6 +423,7 @@ class ImportCreateWithCraminoQcTest(ExecutorTestMixin, TestCaseSnapshot, TestCas
     """
 
     def setUp(self):
+        super().setUp()
         self.maxDiff = None
         self._setUpExecutor(
             CaseImportAction.ACTION_CREATE,
@@ -463,6 +466,7 @@ class ImportCreateWithNgsbitsQcTest(ExecutorTestMixin, TestCaseSnapshot, TestCas
     """
 
     def setUp(self):
+        super().setUp()
         self.maxDiff = None
         self._setUpExecutor(
             CaseImportAction.ACTION_CREATE,

cases_qc/tests/factories.py

@@ -294,83 +294,83 @@ class Meta:
         model = BcftoolsStatsSnRecord
 
     key = factory.Faker("word")
-    value = factory.Sequence(lambda n: n)
+    value = factory.Faker("pyint")
 
 
 class SamtoolsStatsFqRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsFqRecord
 
-    cycle = factory.Sequence(lambda n: n)
-    counts = factory.Sequence(lambda n: [n])
+    cycle = factory.Faker("pyint")
+    counts = factory.Faker("pylist", value_types=[int])
 
 
 class SamtoolsStatsGcRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsGcRecord
 
-    gc_content = factory.Sequence(lambda n: 0.1 * n)
-    count = factory.Sequence(lambda n: n)
+    gc_content = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    count = factory.Faker("pyint")
 
 
 class SamtoolsStatsBasePercentagesRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsBasePercentagesRecord
 
-    cycle = factory.Sequence(lambda n: n)
-    percentages = factory.Sequence(lambda n: [0.1, 0.2, 0.3, 0.4, 0.5, 0.6])
+    cycle = factory.Faker("pyint")
+    percentages = factory.Faker("pylist", value_types=[float])
 
 
 class SamtoolsStatsIsRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsIsRecord
 
-    insert_size = factory.Sequence(lambda n: n)
-    pairs_total = factory.Sequence(lambda n: n)
-    pairs_inward = factory.Sequence(lambda n: n)
-    pairs_outward = factory.Sequence(lambda n: n)
-    pairs_other = factory.Sequence(lambda n: n)
+    insert_size = factory.Faker("pyint")
+    pairs_total = factory.Faker("pyint")
+    pairs_inward = factory.Faker("pyint")
+    pairs_outward = factory.Faker("pyint")
+    pairs_other = factory.Faker("pyint")
 
 
 class SamtoolsStatsHistoRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsHistoRecord
 
-    value = factory.Sequence(lambda n: n)
-    count = factory.Sequence(lambda n: n)
+    value = factory.Faker("pyint")
+    count = factory.Faker("pyint")
 
 
 class SamtoolsStatsIdRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsIdRecord
 
-    length = factory.Sequence(lambda n: n)
-    ins = factory.Sequence(lambda n: n)
-    dels = factory.Sequence(lambda n: n)
+    length = factory.Faker("pyint")
+    ins = factory.Faker("pyint")
+    dels = factory.Faker("pyint")
 
 
 class SamtoolsStatsIcRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsIcRecord
 
-    cycle = factory.Sequence(lambda n: n)
-    ins_fwd = factory.Sequence(lambda n: n)
-    dels_fwd = factory.Sequence(lambda n: n)
-    ins_rev = factory.Sequence(lambda n: n)
-    dels_rev = factory.Sequence(lambda n: n)
+    cycle = factory.Faker("pyint")
+    ins_fwd = factory.Faker("pyint")
+    dels_fwd = factory.Faker("pyint")
+    ins_rev = factory.Faker("pyint")
+    dels_rev = factory.Faker("pyint")
 
 
 class SamtoolsStatsGcdRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsStatsGcdRecord
 
-    gc_content = factory.Sequence(lambda n: 0.1 * n)
-    unique_seq_percentiles = factory.Sequence(lambda n: 0.1 * n)
-    dp_percentile_10 = factory.Sequence(lambda n: 0.1 * n)
-    dp_percentile_25 = factory.Sequence(lambda n: 0.1 * n)
-    dp_percentile_50 = factory.Sequence(lambda n: 0.1 * n)
-    dp_percentile_75 = factory.Sequence(lambda n: 0.1 * n)
-    dp_percentile_90 = factory.Sequence(lambda n: 0.1 * n)
+    gc_content = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    unique_seq_percentiles = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    dp_percentile_10 = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    dp_percentile_25 = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    dp_percentile_50 = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    dp_percentile_75 = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
+    dp_percentile_90 = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
 
 
 class SamtoolsStatsMainMetricsFactory(factory.django.DjangoModelFactory):
@@ -428,22 +428,22 @@ class SamtoolsFlagstatRecordFactory(factory.Factory):
     class Meta:
         model = SamtoolsFlagstatRecord
 
-    total = factory.Sequence(lambda n: n)
-    primary = factory.Sequence(lambda n: n)
-    secondary = factory.Sequence(lambda n: n)
-    supplementary = factory.Sequence(lambda n: n)
-    duplicates = factory.Sequence(lambda n: n)
-    duplicates_primary = factory.Sequence(lambda n: n)
-    mapped = factory.Sequence(lambda n: n)
-    mapped_primary = factory.Sequence(lambda n: n)
-    paired = factory.Sequence(lambda n: n)
-    fragment_first = factory.Sequence(lambda n: n)
-    fragment_last = factory.Sequence(lambda n: n)
-    properly_paired = factory.Sequence(lambda n: n)
-    with_itself_and_mate_mapped = factory.Sequence(lambda n: n)
-    singletons = factory.Sequence(lambda n: n)
-    with_mate_mapped_to_different_chr = factory.Sequence(lambda n: n)
-    with_mate_mapped_to_different_chr_mapq5 = factory.Sequence(lambda n: n)
+    total = factory.Faker("pyint")
+    primary = factory.Faker("pyint")
+    secondary = factory.Faker("pyint")
+    supplementary = factory.Faker("pyint")
+    duplicates = factory.Faker("pyint")
+    duplicates_primary = factory.Faker("pyint")
+    mapped = factory.Faker("pyint")
+    mapped_primary = factory.Faker("pyint")
+    paired = factory.Faker("pyint")
+    fragment_first = factory.Faker("pyint")
+    fragment_last = factory.Faker("pyint")
+    properly_paired = factory.Faker("pyint")
+    with_itself_and_mate_mapped = factory.Faker("pyint")
+    singletons = factory.Faker("pyint")
+    with_mate_mapped_to_different_chr = factory.Faker("pyint")
+    with_mate_mapped_to_different_chr_mapq5 = factory.Faker("pyint")
 
 
 class SamtoolsFlagstatMetricsFactory(factory.django.DjangoModelFactory):
@@ -469,9 +469,9 @@ class Meta:
         model = SamtoolsIdxstatsRecord
 
     contig_name = factory.Faker("word")
-    contig_len = factory.Sequence(lambda n: n)
-    mapped = factory.Sequence(lambda n: n)
-    unmapped = factory.Sequence(lambda n: n)
+    contig_len = factory.Faker("pyint")
+    mapped = factory.Faker("pyint")
+    unmapped = factory.Faker("pyint")
 
 
 class SamtoolsIdxstatsMetricsFactory(factory.django.DjangoModelFactory):
@@ -496,15 +496,15 @@ class Meta:
         model = CraminoSummaryRecord
 
     key = factory.Faker("word")
-    value = factory.Sequence(lambda n: n)
+    value = factory.Faker("pyint")
 
 
 class CraminoChromNormalizedCountsRecordFactory(factory.Factory):
     class Meta:
         model = CraminoChromNormalizedCountsRecord
 
     chrom_name = factory.Faker("word")
-    normalized_counts = factory.Sequence(lambda n: 0.1 * n)
+    normalized_counts = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
 
 
 class CraminoMetricsFactory(factory.django.DjangoModelFactory):
@@ -529,7 +529,7 @@ class Meta:
         model = NgsbitsMappingqcRecord
 
     key = factory.Faker("word")
-    value = factory.Sequence(lambda n: 0.1 * n)
+    value = factory.Faker("pyfloat", min_value=0.0, max_value=1.0)
 
 
 class NgsbitsMappingqcMetricsFactory(factory.django.DjangoModelFactory):

cases_qc/tests/helpers.py

@@ -1,9 +1,12 @@
 import datetime
 import json
+import random
 import typing
 from unittest import mock
 import uuid
 
+import factory
+
 
 def extract_from_dict(vals: typing.Any, keys: typing.Iterable[str]) -> dict[str, typing.Any]:
     """Helper to extract certain values from the dictionary."""
@@ -38,3 +41,41 @@ def default(self, obj):
 def flatten_via_json(data: dict) -> dict:
     """Flatten a dictionary by converting it to JSON and back."""
     return json.loads(json.dumps(data, cls=FlattenEncoder))
+
+
+def fake_urandom(size: int, /) -> bytes:
+    """Fake version of urandom that uses random."""
+    return bytes(random.randint(0, 255) for _ in range(size))
+
+
+class FixRandomSeedMixin:
+    def setUp(self):
+        """Set fixed seeds."""
+        super().setUp()
+        # determine the seed
+        seed = getattr(self, "__fixrandomseed_fixed_seed", 42)
+        # seed the random module and keep state for recovery
+        self._FixRandomSeedMixin__random_state = random.getstate()
+        random.seed(seed)
+        # patch all factory.Faker random states
+        self._FixRandomSeedMixin__faker_generators = []
+        default_faker = factory.Faker._get_faker()
+        for the_factory in default_faker.factories:
+            self._FixRandomSeedMixin__faker_generators.append(the_factory._Generator__random)
+            the_factory._Generator__random = random.Random(seed)
+        # patch the os.urandom function
+        self._FixRandomSeedMixin_patcher = mock.patch("os.urandom", new=fake_urandom)
+        random.seed(seed)
+
+    def tearDown(self):
+        """Reset the random state"""
+        super().tearDown()
+        # recover all factory.Faker random states
+        default_faker = factory.Faker._get_faker()
+        for the_factory, generator in zip(default_faker.factories, self._FixRandomSeedMixin__faker_generators):
+            the_factory._Generator__random = generator
+        # recover the random module's state
+        random.setstate(self._FixRandomSeedMixin__random_state)
+        # recover the os.urandom function
+        self._FixRandomSeedMixin_patcher.stop()
+        random.setstate(self._FixRandomSeedMixin__random_state)